โครโมโซมวายกับการศึกษาวิวัฒนาการของมนุษย์ (Y chromosome and the study of human evolution)

Authors

  • Wibhu Kutanan Khon Kaen University
  • Daoroong Kangwanpong Chiang Mai University

DOI:

https://doi.org/10.14456/tjg.2014.2

Keywords:

Y chromosome, haplogroup, lineage, human evolution, East Asia

Abstract

การถ่ายทอดพันธุกรรมของโครโมโซมวายของมนุษย์ไปสู่รุ่นถัดไปนั้นเป็นการถ่ายทอดผ่านทางฝ่ายชายเท่านั้น และเนื่องจากดีเอ็นเอส่วนใหญ่ของโครโมโซมวายไม่เกิดรีคอมบิเนชั่นในระหว่างการแบ่งเซลล์แบบไมโอซิส  จึงทำให้ดีเอ็นเอเกือบทั้งหมดของโครโมโซมวายถ่ายทอดจากพ่อสู่ลูกชาย คุณสมบัติพิเศษดังกล่าวทำให้โครโมโซมวายเป็นเครื่องหมายทางพันธุกรรมที่ได้รับการพิสูจน์แล้วว่ามีประสิทธิภาพสำหรับติดตามประวัติการสืบเชื้อสายทางฝ่ายชายของมนุษย์  บทความนี้กล่าวถึงโครงสร้างของโครโมโซมวาย รูปแบบของความผันแปร และปัจจัยที่ส่งผลต่อความผันแปรในดีเอ็นเอของโครโมโซมวาย นอกจากนี้ยังอธิบายถึงวิธีการศึกษาแฮโปลกรุ๊ป  การตั้งชื่อและการจัดกลุ่มเพื่อใช้สืบเชื้อสายของโครโมโซมวาย ข้อมูลการกระจายของแฮโปลกรุ๊ปที่สนับสนุนทฤษฎีการอพยพออกจากแอฟริกาของมนุษย์ปัจจุบัน และยังสามารถเชื่อมโยงเส้นทางการอพยพที่อาจเป็นไปได้ในช่วงแรกขณะเข้าสู่เอเชียตะวันออก นอกจากนั้นยังกล่าวถึงโครงสร้างพันธุกรรมของประชากรเอเชียตะวันออกในปัจจุบัน  ท้ายที่สุดจะกล่าวถึงแนวทางการพัฒนางานวิจัยโครโมโซมวายในอนาคต เพื่อไขปริศนาประวัติศาสตร์ที่ซับซ้อนของมนุษย์ในยุคปัจจุบัน

 

The human Y chromosome is exclusively paternally inherited and most of its DNA does not undergo recombination during meiosis, resulting in transmission of the whole chromosome from father to son. These special features make the Y chromosome an efficient tool for inferring human population history in paternal lineage.  This review article described the Y chromosomal structure, pattern of polymorphisms and factors that affect polymorphisms.  Moreover, methods for studying Y chromosome haplogroup, like designation and classification for investigating paternal lineage, are reviewed.  Information of the Y chromosomal haplogroup distributions support the Out-of-Africa theory and can be used to predict the migration history of the current human species into East Asia.  The present genetic structure of East Asian populations is also reviewed.  Finally, we discussed the possibility of developing the study of the Y chromosome for unraveling the complex history of modern human populations

References

วิภู กุตะนันท์ (2555) ดีเอ็นเอไมโทคอนเดรีย: เครื่องมือติดตามประวัติการสืบเชื้อสายประชากร วารสารวิทยาศาสตร์ มข 40: 708–719.

Bermúdez de Castro JM, Arsuaga JL, Carbonell E, Rosas A, Martínez I, Mosquera M (1997) A hominid from the lower Pleistocene of Atapuerca, Spain: possible ancestor to Neandertals and modern humans. Science 276: 1392–1395.

Berta P, Hawkins JR, Sinclair AH, Taylor A, Griffiths BL, Goodfellow PN, Fellous M (1990) Genetic evidence equating SRY and the testis determining factor. Nature 348: 448–450.

Besaggio D, Fuselli S, Srikummool M, Kampuansai J, Castrì L, Tyler-Smith C, Seielstad M, Kangwanpong D, Bertorelle G (2007) Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differences. BMC Evol Biol 7 (Suppl 2): S12.

Bowler JM, Johnston H, Olley JM, Prescott JR, Roberts RG, Shawcross W, Spooner NA. (2003) New ages for human occupation and climatic change at Lake Mungo, Australia. Nature 421: 837–840.

Brion M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Borsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider PM, et al. (2005) Introduction of an single nucleotide polymorphism-based “Major Y-chromosome haplography typing kit” suitable for predicting the geographical origin of male lineages. Electrophoresis 26: 4411–4420.

Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, et al. (2011) Genographic Consortium: Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS One 6: e24282.

Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325: 31–36.

Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM (2009) The last glacial maximum. Science 325: 710–714.

Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, Halos SC, Gunnarsdóttir E, Myles S, Hughes DA, et al. (2011) The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negritogroups. Eur J Hum Genet 19: 224–230.

Gabunia L. Vekua A, Lordkipanidze D, Swisher CC 3rd, Ferring R, Justus A, Nioradze M, Tvalchrelidze M, Antón SC, Bosinski G,et al. (2000) Earliest Pleistocene hominid cranial remainsfrom Dmanisi, Republic of Georgia: taxonomy, geological setting, and age. Science 288: 1019–1025.

Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, UnderhillPA, Cavalli-Sforza LL, Herrera RJ (2007) The Himalayas as a directional barrier to gene flow. Am J Hum Genet 80: 884–894.

Goebel T (1999) Pleistocene human colonization of Siberia and peopling of the Americas: an ecological approach. Evol Anthropol 8: 208–227.

Hammer MF (1994) A recent insertion of an alu element on the Y chromosome is a useful

marker for human population studies. Mol Biol Evol 11: 749–761.

Hammer MF (1995) A recent common ancestry for human Y chromosomes. Nature 378: 376–378.

Hammer MF, Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S (2006) Dual origins of the Japanese: common ground for hunter-gatherer andfarmer Y chromosomes. J Hum Genet 51: 47–58.

Hammer MF, Karafet T, Rasanayagam A, Wood ET, Altheide TK, Jenkins T, Griffiths RC,

Templeton AR, Zegura SL (1998) Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol Biol Evol 15: 427–441.

Jobling MA, Bouzekri N, Taylor PG (1998) Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1). Hum Mol Genet 7: 643–653.

Jobling MA, Samara V, Pandya A, Fretwell N, Bernasconi B, Mitchell RJ, Gerelsaikhan T, Dashnyam B, Sajantila A, Salo PJ, et al. (1996) Recurrent duplication and deletion polymorphisms on the long arm of the Y chromosome in normal males. Hum Mol Genet 5: 1767–1775.

Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4: 598–612.

Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18: 830–838.

Karafet TM, Xu L, Du R, Wang W, Feng S, Wells RS, Redd AJ, Zegura SL, Hammer MF (2001) Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am J Hum Genet 69: 615–628.

Kayser M, Brauer S, Cordaux R, Casto A, Lao O, Zhivotovsky LA, Moyse-FaurieC, Rutledge RB, Schiefenhoevel W, Gil D, et al. (2006) Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Mol Biol Evol 23: 2234–2244.

Kayser M, Brauer S, Weiss G, Schiefenhövel W,Underhill PA, Stoneking M (2001) Independent histories of human Y chromosomes from Melanesia and Australia. Am J Hum Genet 68: 173–190.

Krausz C, Quintana-Murci L, Rajpert-De Meyts E,

JørgensenN, Jobling MA, Rosser ZH, SkakkebaekNE, McElreaveyK (2001) Identification of a Y chromosome haplogroup associated with reduced sperm counts. Hum Mol Genet 10: 1873–1877.

Manica A, Prugnolle F, Balloux F (2005) Geography is a better determinant of human genetic differentiation than ethnicity. Hum Genet 118: 366–371

Mellars P (2002) Archaeology and the origins of modern humans: European and African perspectives. Proc Brit Acad 106: 31–47.

Mellars PA (2002) In: Crow TJ (eds) The Speciation of Modern Homo sapiens. Oxford Univ. Press, Oxford, UK, pp 31–47.

Nachman MW, Crowell SL (2000) Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297–304.

Oota H, Settheetham-Ishida W, Tiwawech D, Ishida T, Stoneking M (2001) Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nature Genet 29: 20–21.

Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA 102: 15 942–15 947.

Roewer L, Arnemann J, Spurr NK, Grzeschik KH, Epplen JT (1992) Simple repeat sequences on

the human Y-chromosome are equally polymorphic as their autosomal counterparts. Hum Genet 89: 389–394.

Rootsi S, Zhivotovsky LA, Baldovic M, Kayser M, Kutuev IA, Khusainova R, Bermisheva MA, Gubina M, Fedorova SA, Ilumäe AM, et al. (2007) A counter-clockwise northern route of the Ychromosome haplogroup N from Southeast Asia towards Europe. Eur J Hum Genet 15: 204–211.

Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES (2006) Positive natural selection in the human lineage. Science 312: 1614–1620

Scholes C, Siddle K, Ducourneau A, Crivellaro F, Järve M, Rootsi S, Bellatti M, Tabbada K, Mormina M, Reidla M, et al. (2011) Genetic diversity and evidence for population admixture in BatakNegritos from Palawan

. Am J Phys Anthropol 146: 62–72.

Seielstad MT, Minch E, Cavalli-Sforza LL (1998) Genetic evidence for a higher female migration rate in humans. Nature Genet 20: 278–280.

Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE, LinAA, Mitra M, Sil SK, Ramesh A, et al. (2006) Polarity and temporality of high-resolutiony-chromosome distributions in India identify both indigenous andexogenous expansions and reveal minor genetic influence of CentralAsian pastoralists. Am J Hum Genet 78: 202–221.

Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, Jin L, Su B (2005) Y-chromosome evidence of southern origin of the East Asian specific haplogroup O3-M122. Am J Hum Genet 77: 408–419.

Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RL, Xiao CJ, et al. (2008) Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol 6: 45.

Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans.

Science 239: 1263–1268.

Su B, Jin L, Underhill P, Martinson J, Saha N, McGarvey ST, Shriver MD, Chu J, Oefner P, Chakraborty R, et al. (2000) Polynesian origins: insights from the Y chromosome. Proc Natl Acad Sci USA 97: 8225–8228.

Sun C, Skaletsky H, Birren B, Devon K, Tang Z, Silber S, Oates R, Page DC (1999) An azoospermic man with a de novo point mutation in the Y-chromosomal gene USP9Y. Nature Genet 23: 429–432.

Swisher CC3rd, Curtis GH, Jacob T, Getty AG, Suprijo A, Widiasmoro (1994) Age of the earliest known hominids in Java, Indonesia. Science 263: 1118–1121.

Templeton A (2002) Out of Africa again and again. Nature 416: 45-51.

Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, Underhill PA, Pierson M, Frame IG, Hagelberg E (2003) Genetic affinities of the Andaman Islanders, a vanishing human population. Curr Biol 13: 86–93.

Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW (2000) Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci USA 97: 7360–7365.

Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ (1997) Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res 7: 996–1005.

Underhill PA, Kivisild T (2007) Use of Y chromosome and mitochondrial DNA population structure in tracing human migration. Annu Rev Genet 41: 539–564.

Valladas H, Joron JL, Valladas G, Arensburg B, Bar-Yosef O, Belfer-Cohen A, Goldberg P , Laville H, Meignen L, Rak Y,et al.(1987) Thermoluminescence dates for the Neanderthal burial site at Kebara in Israel. Nature 330: 159–160.

Valladas H. Reyss JL, Joron JL, Valladas G, Bar-Yosef O, Vandermeersch B (1998)

Thermoluminescence dating of Mousterian ‘proto-Cro-Magnon’ remains from Israel and the origin of modern man. Nature 331: 614–616.

Wang CC, Li H (2013) Inferring human history in East Asia from Y chromosomes. Investigative Genetics 4: 11.

Wang CC, Yan S, Qin ZD, Lu Y, Ding QL, Wei LH, Li SL, Yang YJ, Jin L, Li H, et al. (2013) Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611. J Syst Evol 3: 280–286.

Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, Gao Y, Mao X, Zhang L, et al. (2004) Genetic evidence supports demic diffusion of Han culture. Nature 431: 302–305.

Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y, et al. (2009) Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree, Curr Biol 19: 1453–1457.

Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, Du R, Fu S, Li P, Hurles ME, et al. (2006) Male

demography in East Asia: a north–south contrast in human population expansion times. Genetics 172: 2431–2439.

Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups Genome Res 12: 339–348.

Yan S, Wang CC, Li H, Li SL, Jin L (2100) Genographic Consortium: An updated tree of Y-chromosome haplogroup O and revised phylogenetic positions of mutations P164 and PK4. Eur J Hum Genet 19: 1013–1015.

Zerjal T, Pandya A, Thangaraj K, Ling EY, Kearley J, Bertoneri S, Paracchini S, Singh L, Tyler-Smith C (2007) Y-chromosomal insights into the genetic impact of the caste system in India. Hum Genet 121: 137–144.

Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, Qamar R, Ayub Q, Mohyuddin A, Fu S, et al. (2003) The genetic legacy of the Mongols. Am J Hum Genet 72: 717–721.

Zhong H, Shi H, Qi XB, Xiao CJ, Jin L, Ma RZ, Su B (2010) Global distribution of Ychromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 55: 428–435.

http://www.cstl.nist.gov/biotech/strbase/ystrpos1.htm

http://www.isogg.org/tree/

http://www.yhrd.org/index.html

Downloads

Published

2014-08-31

Issue

Section

Review Articles